Re: [AMBER] AmberTools serial compilation with intel compiler 12.0.0: final link failed

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 1 Dec 2010 09:29:59 -0500

In addition to what Dan said, did you source the intel environment scripts
(ifortvars.sh, iccvars.sh, they should be in the same directory as ifort and
icc)? They set up LD_LIBRARY_PATH and PATH for you. However, I can verify
that the intel compilers version 11.1.069 works for installing Amber on my
machine, so if you can roll back, I would suggest trying that to see if it
works.

Good luck!
Jason

On Wed, Dec 1, 2010 at 8:49 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> Hi,
>
> Do you have any previous versions of the intel compiler, and if so
> does compilation complete with them?
>
> Also, could you paste the last 20 or so lines leading up to the error?
> A brief web search suggests this may be related to the '-lsvml' flag
> during the link step (however the post refers to version 11.1 so no
> guarantees, http://software.intel.com/en-us/forums/showthread.php?t=77211
> ).
> Intel is notorious for messing with the linking step (see their MKL
> stuff for more linking headaches) so I'm not surprised something may
> have broken in the new version of the compilers.
>
> Anyway, you could try manually editing your config.h file to remove
> the '-lsvml' flag from the FLIBSF variable and see if compilation is
> able to proceed.
>
> -Dan
>
> On Wed, Dec 1, 2010 at 6:34 AM, Vlad Cojocaru
> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> > Dear Amber community,
> >
> > I am compiling AMBER 11 with the Intel compiler 12.0.0 (which I just
> > purchased)
> > The linking during the *SERIAL* compilation of Amber Tools 1.4 (patched
> > with all bugfixes as of today) fails with error (see below, no other
> > error in make.log):
> >
> > Has anybody experienced this with this version of the Intel compiler?
> > I would appreciate any ideas on how to get rid of this problem
> >
> > Best
> > Vlad
> >
> >
> > Details:
> > -------
> > Architecture
> > Linux name 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 12:54:20 EST 2010
> > x86_64 x86_64 x86_64 GNU/Linux
> > CPU:
> > 2xAMD 6-core opterons per node
> > OS:
> > CentOS 5.5 (RHL 5.5)
> > Compiler
> > Intel 2011-0-084 (version 12)
> > Config.h file attached
> >
> >
> > make error:
> > ---------------------------
> > ld: pbsa: hidden symbol `__intel_cpu_indicator_init' in
> >
> /usr/global/intel/composerxe-2011.0.084/compiler/lib/intel64/libirc.a(cpu_disp.o)
> > is referenced by DSO
> > ld: final link failed: Nonrepresentable section on output
> > make[1]: *** [pbsa] Error 1
> > make[1]: Leaving directory
> >
> `/usr/global/amber/intel-2011.0.084-openmpi-1.5/amber11/AmberTools/src/pbsa'
> > make: *** [serial] Error 2
> > --------------------------------------
> >
> >
> >
> > --
> > Dr. Vlad Cojocaru
> > Max Planck Institute for Molecular Biomedicine
> > Department of Cellular and Developmental Biology
> > Roentgenstrasse 20
> > 48149 Muenster, Germany
> > tel: +49-251-70365-324
> > fax: +49-251-70365-399
> > email: vlad.cojocaru[at]mpi-muenster.mpg.de
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Dec 01 2010 - 07:00:04 PST
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